BMAL1 p.Ala2=
c.6A>T · rs75830309 · VCV709842
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.62%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -5 |
| Overall | ||
| CADD | 3.948 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.62%
African / African-American · 1,956/74,768 alleles
Filtering AF
2.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.48%
Overall
0.139%
2,224/1,604,866 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.62% | 38 |
| Remaining individualsnot grpmax-eligible | 0.214% | 467 |
| Admixed American | 0.159% | 629 |
| Middle Eastern | 0.0828% | 1,208 |
| South Asian | 0.00446% | 22,429 |
| European (non-Finnish) | 0.00272% | 36,714 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BMAL1
- Protein
- p.Ala2=
- Coding
- c.6A>T
- MANE Select
- NM_001297719
- dbSNP
- rs75830309
- Type
- single nucleotide variant
- Location
- chr11:13354314 (GRCh38)
- Structure
- AlphaFold pLDDT 67.00 · 3 PDB
- Residue 2
- the 'disordered' region
Similar variants
- BMAL1 c.140+7C>T Uncertain significance ★ same type
- BMAL1 p.Ala359Pro Uncertain significance ★ ⚠ same type
- BMAL1 p.Arg166Ter Uncertain significance ★ same type
- BMAL1 p.Arg238Gly Uncertain significance ★ ⚠ same type
- BMAL1 p.Arg276Ter Uncertain significance ★ same type
- BMAL1 p.Arg343Trp Uncertain significance ★ ⚠ same type
- BMAL1 p.Arg37Cys Uncertain significance ★ ⚠ same type
- BMAL1 p.Arg497Gln Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bmal1-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown